I would keep the original dial as the patina you mention (not really rust right?) may be considered very attractive to many of us. If the original dial has merely a cosmetic problem and nothing to impair the operation of the watch, I would keep it ON the watch. If it really bothers you, then replace the dial with the newer style, but ask AP for the old dial to keep with the watch for the future in case you change your mind.
The problem with replacing the dial is that the AP logo will be now in a different location, and for many AP RO fans, the placement of the AP logo is a defining characteristic of the early series ROs, differentiating it from later series and making it instantly recongizable to those who really know the ROs. I also typically argue against part replacements like this as you sometimes end up with a "Frankenwatch," but mine is just one opinion and others will put forth very good arguments for making such changes.
Can you please post a photo so we can see what the dial looks like?
In any case, good luck with the servicing on your wonderful RO.
respo